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Jean M
01-03-2014, 08:59 PM
Hidden away in the supplementary information of Kay Prüfer et al., The complete genome sequence of a Neanderthal from the Altai Mountains, Nature http://www.anthrogenica.com/showthread.php?1728-Complete-Genenome-of-Neanderthal-from-the-Altai-Mountains-%28-Pr%FCfer-2013%29 is a list of 87 genes in which protein coding changes are seen in present-day humans, but which differ from Neandertal, Denisovan and the great apes.

Ian Sample, science correspondent for The Guardian picked up on this in December.


Scientists draw up definitive list of genes that make us human
Genetic changes that distinguish us from Neanderthals could throw light on how humans came to dominate planet

Researchers have drawn up the first definitive list of genetic changes that make modern humans different from our nearest ancient ancestors, who died out tens of thousands of years ago. The list amounts to a series of biological instructions that shape the brains and bodies of living people and distinguish them from Neanderthals and other early humans that lived alongside them.

Scientists are now going through the list to work out which genetic tweaks might have been most important in driving modern humans to become the most dominant living organism on the planet today. "We are quite confident that among these genetic changes lie the basis for the interesting differences between modern humans and Neanderthals," said Janet Kelso, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig. These mutations are specific to modern humans. Are they responsible for some of the features we have, or some of our particular achievements, such as settling all over the planet, or flying aeroplanes?" said Kay Prüfer, the first author on the study. "I don't think we will ever find an aeroplane gene, but maybe we will find something that makes our brains tick better. If something like that exists, it will be on this list."

http://www.theguardian.com/science/2013/dec/18/scientists-list-genes-make-us-human-neanderthals

From the Prüfer et al. supplementary information, pp. 194-5:


The catalogs of changes unique to either the modern or archaic human lineages can serve as a first step in identifying those genes and biological systems that were most important in recent human evolutionary history. Among non-synonymous changes, we see enrichment for genes affecting melanocyte development in the modern-specific catalog (Table S18.5), and different musculoskeletal and hair morphologies in the archaic-specific catalog (Table S18.6). We explore some of these enrichments in more detail in a companion study with the addition of 2 Neandertal exomes, to obtain a higher resolution for the allelic state of these non-synonymous changes in archaic human groups. Among genes with changes in 3’ UTR regions in the modern-specific catalog (Table S18.5), we also
observe enrichments for particular skeletal morphologies, including limb length, as well as morphologies of the larynx and the epiglottis which are involved in speech production. We note, however, that Neandertals are known to have had hyoid bones that were virtually identical to those of modern humans, which makes it likely that the anatomical structures necessary for human speech had already evolved before the Neandertal and modern human lineages split....

The catalogs we provide here are the complete set of genetic changes that distinguish modern and archaic humans from their common ancestor, and will allow the genetic processes that led to the evolution of the modern human and archaic human forms to be explored. As a first step, we have identified changes on the modern human lineage that fall within regions that we identify as having been affected by selective sweeps on the modern human lineage (SI 19b). Future functional genomic analyses may serve to further expand the insights we can gain from archaic human sequence data, with respect to both our own recent evolution and the evolution of other extinct human groups.

parasar
01-03-2014, 09:29 PM
In the Meyer et al Denisova paper too such genes were mentioned.


We note that among the 23 most conserved positions affected by amino acid changes (primate conservation score ≥ 0.95), eight affect genes that are associated with brain function or nervous system development (NOVA1, SLITRK1, KATNA1, LUZP1, ARHGAP32, ADSL, HTR2B, CBTNAP2). Four of these are involved in axonal and dendritic growth (SLITRK1, KATNA1) and synaptic transmission (ARHGAP32, HTR2B ) and two have been implicated in autism (ADSL, CBTNAP2). CNTNAP2 is also associated with susceptibility to language disorders (27) and is particularly noteworthy as it is one of the few genes known to be regulated by FOXP2, a transcription factor involved in language and speech development as well as synaptic plasticity (28). It is thus tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans.

http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2012_Science_Meyer_DenisovaSeq.pdf

Jean M
01-03-2014, 09:57 PM
Yes I cited them in AJ on that topic, but the latest paper takes us a bit further.

Tomenable
03-15-2016, 10:42 PM
regions that we identify as having been affected by selective sweeps on the modern human lineage

I'm surprised by this selective sweep (it is strange how did it occur in Papuans, Europeans, and Middle Easterners - but not other groups):

http://psych.colorado.edu/~carey/pdfFiles/BrainSizeASPM_Lahn.pdf

https://en.wikipedia.org/wiki/ASPM_(gene)#Evolution

https://en.wikipedia.org/wiki/Papuan_people#Genetics

But it is an old study from 2005 - maybe they were wrong when claiming that this new allele is so young?

If it is so young, how did it spread to both Papua New Guinea and Western Eurasia at the same time?

It also seems, that scientists don't really know what it does, and what is so advantageous about it.

miiser
03-16-2016, 12:29 AM
Among genes with changes in 3’ UTR regions in the modern-specific catalog (Table S18.5), we also observe enrichments for particular skeletal morphologies, including limb length, as well as morphologies of the larynx and the epiglottis which are involved in speech production. We note, however, that Neandertals are known to have had hyoid bones that were virtually identical to those of modern humans, which makes it likely that the anatomical structures necessary for human speech had already evolved before the Neandertal and modern human lineages split....

This is a worthwhile investigation, but I think it's hyperbole to label these as the genes that "make us human" or "wise". Would someone born today with shorter limbs be considered non human? I've known people with short limbs, and they're still given ID cards (just as if they were real humans!) in spite of their obvious inferiority. As pointed out in the article, features such as human speech were already well established before the Neanderthal branch.

Following the layman's usage of the term "human", what little evidence we have suggests that Neanderthals behaved as humans in all the important ways that set us apart from the beasts. Following a technical scientific usage, "human" is used to refer to the Homo genus (latin for "human"), which includes Neanderthal. And while "sapiens" is latin for "wise", it is debatable whether this is really a unique defining feature of modern Homo sapiens. It is not even settled whether Neanderthal is more properly considered a subspecies of Homo sapiens or a distinct species of Homo.

Because Homo neanderthalensis got absorbed into Homo sapiens, it is reasonable to assume that there were one or more differing characteristics that put Neanderthals at a disadvantage against Homo sapiens. But to consider Neanderthal as non human is a stretch. At most, one could say that these are the genes that make us modern, and maybe, possibly a little better.